Excessive amounts of heavy metals adversely affect plant growth and development. Also, the presence of elevated levels of heavy metal ions triggers a wide range of cellular responses including changes in gene expression and synthesis of metal-detoxifying peptides. The overall objective of this research was to elucidate some microscopic effects of heavy metals on the formation, development, and structure of ovule and seed storage proteins in Chenopodium botrys L. To achieve this purpose, the surrounding area of Hame-Kasi iron and copper mine (Hamedan, Iran) was chosen as a polluted area where the amount of some heavy metals was several times higher than the natural soils. Flowers and young pods were removed from nonpolluted and polluted plants, fixed in FAA 70 and subjected to developmental studies. Our results showed that heavy metals can cause some abnormalities during the ovule developmental process. Decreasing the size of embryo sac, quick growth of inner integument, quick degradation of embryonic sac cells, accumulation of dark particles, irregularity, and even blockage of the nuclear envelope formation and increasing of embryonic sac cytoplasm concentration were the effects of heavy metals. Reduction of ovule number was also seen in the plants collected from polluted area. For protein studies, mature seeds were harvested from nonpolluted and polluted plants at the same time. Seed storage proteins (water soluble ones) were extracted and studied by sodium dodecyl sulfate-polyacrylamide gel electrophoresis after being prepared. The results revealed that there were no significant differences between seed protein bands of polluted and nonpolluted samples, but the quantity of protein bands was different, and there was a slight quantitative increase of bands with molecular mass of 35 and 15 kD and decrease of a band with molecular mass of 17 kD in the plants collected from the mine area.